[2] The walls of the Bombay Fort were demolished in 1862 and the gate leading to the church was replaced by the Flora Fountain in 1864.

One of the gates in the fort which the East India Company had built to protect their settlement was the entrance to the St. Thomas Church.

Gerald Aungier was placed in charge of the British East India Company's newly acquired factories at Surat and Bombay, which had until then belonged to Portugal.

As governor of Bombay from 1672 to 1677, Angier built a church, a hospital, a court of justice and other civic amenities on the English model, and fortified the company's commercial establishment.

[4] The foundation stone for the church was laid in 1676, on Bombay Green, at the present site of the St. Thomas' Cathedral, but over 40 years elapsed before construction could be completed.

[7] The church was consecrated as a cathedral in July 1837 concurrent with the appointment of the first Bishop of Bombay, Thomas Carr.

[10] The cathedral contains many carved stone memorials from the eras of Company rule in India and the British Raj.

[3][14][15] After completion of a major restoration work the cathedral was selected in 2004 for a UNESCO Asia-Pacific heritage conservation award.